# Test6 fmriprep-rc4 with MNI Pediatric template on cluster  
import subprocess

!export SINGULARITYENV_TEMPLATEFLOW_HOME=/imaging/jj02/CALM/templateflow

for n in range(1):
    p = subprocess.Popen(("sbatch", "--mem-per-cpu=64gb", "--job-name=fmriprep", #sbatch cmd
                          "--output", "/imaging/jj02/CALM/slurm/fmriprep_child_test6.out",
                          "singularity", "run", "-C", #singularity call
                          "-B", "/imaging/jj02/CALM:/CALM,/imaging/projects/cbu/calm/CALM_BIDS_New:/CALM_BIDS_New",
                          "-B", "/scratch/$USER/templateflow:/imaging/jj02/CALM/templateflow",
                          "/imaging/local/software/singularity_images/fmriprep/fmriprep-1.4.1rc4.simg",
                          "/CALM_BIDS_New", 
                          "/CALM_BIDS_New/derivatives/fmriprep_child_test6", #dirs
                          "participant", "--participant_label", '%03d' %(n+1), #fmriprep options
                          "-v", "-w", "/CALM_BIDS_New/derivatives/fmriprepwork_child_test6",
                          "--skull-strip-template", "MNIPediatricAsym:cohort-1"
                          "--output-spaces", "MNIPediatricAsym:cohort-1", 
                          "--fs-no-reconall",
                          "--fs-license-file", "/CALM/license.txt",
                          "--notrack"),
                         shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE)